Please confirm that I was wrong on this classification. I put cytoskeleton (cytokinetic bridge) because to the top right of the bottom-most cell I clearly see one. Let me know if my eyes are playing tricks.

Posted - 2016.03.25 01:23:26 -
[122] - Quote
IMO although the kinetic bridge shape is there (in red), it's not lit up in green, so I wouldn't have chosen it as an answer.

What they're doing is they're coloring in green one protein at a time, and then we're supposed to identify where in the cell the green protein is hiding. So a cell can have a nucleus, cytoplasm, and a kinetic bridge, but if none of those are green (or with dots), then the protein that that sample is about is not there.

Please confirm that I was wrong on this classification. I put cytoskeleton (cytokinetic bridge) because to the top right of the bottom-most cell I clearly see one. Let me know if my eyes are playing tricks.

Posted - 2016.03.26 18:43:45 -
[130] - Quote
Great idea to post these, I'm also having a hard time nailing down some of the samples and I'm starting to realize why this was released as a mini game. I wish there was a way to do this in game, to share samples or somehow team up and work together. I'm new to the mini game and also to cell research, not my profession, but I am a visual artist and I am very good at spotting patterns and colors. So far I have a decent rate of correct guesses but I always get samples which surprise me and the correct answer is puzzling based on the description.

I guess we could just use teamspeak, form a fleet and post images online to try and reach a better consensus and also learn to better identify these. I know I could definitely use a mentor on this one.

I got the exact same image and totally agree with your classification. I did the same.

I wonder how much screwed the baseline is due to the community consensus approach. Is there anything known on how they avoid those effects?

CheersRakin

They use data analysis and draw up graphs of the likelihood of 'incorrect result' from the community based on percentage consensus. Draw a graph and pick a 'cut-off' consensus for which they will accept as the community being correct. As with all science, some of the results will be wrong, but they will be able to minimise this as required. They can even estimate their error rate with reasonable precision.

Data can also be cleaned up by removing all data entries by repeat offenders of the 'cytoplasm, nucleus' trick. Additionally, they can opt to look at data from the 90%+ graded players where overall community consensus is middling. There are many ways they can improve their data set to obtain best results.

Please confirm that I was wrong on this classification. I put cytoskeleton (cytokinetic bridge) because to the top right of the bottom-most cell I clearly see one. Let me know if my eyes are playing tricks.

Classification Result says: "Nuclear Speckles"; it sure looks like "Nucleoplasm" to me.

What's the deal here? Is this faint variation enough to declassify it as "nucleoplasm" and flag it as "nuclear speckles"?

If so, some explaining text would be appreciated with those very hard to understand "teaching moments".

Thank you! :)

This is also one of the known errors, it should indeed be nucleoplasm and nuclear speckles (at first we thought they were mutually exclusive, which is why this one happened). It will be corrected asap.

I had an image analysed by a professional today:http://imgur.com/8cy3D7m
How much difference in intensity is needed to be correct with Cell-to-Cell-Variations? Or was the professional wrong?

I would be hesitant to call that variation as all strongly stained cells are in the bottom left part of the image. That makes me think it's possible (likely) that the plate was not perfectly adjusted when imaging, and that the cells were imaged at different focal planes, e.g. the stronger green ones were imaged more in the middle of the nucleus, making the staining appear stronger, and the weaker ones at higher up/lower > making the staining appear less strong.

Sample 100000440 has been defined as 100% Vesicles, and I regret not making this choice, in addition to Rods and Rings. I picked R&R because I saw a few rod-like structures... am I completely wrong, or could this sample contain both R&R and Vesicles? Must complete ring structures be present, in samples with R&R? I've marked the BG views with arrows.

Sample 100000264 has been defined as 100% Cytoplasm, but I wonder what the structures that seem to outline some parts of the cells might be, marked with arrows in my Green-only screenshot. I thought they might represent a plasma membrane.

The first image was a really tricky sample, and I agree it kinda looks like R&R, but not really. Some type of vesicles have this elongated pattern that you can see here. We'll try to remove it from the training set.

For the second image, I see what you mean, but I don't think it's plasma membrane. The cells you look at is a type of brain cell (called U-251 MG), which is known for having what (at least we call) "membrane blebbing", which is that kind of thick edge at the membrane. If you toggle red/green on off you'd likely see a good overlap of the red/green, although the red might be weaker there.

I had an image analysed by a professional today:http://imgur.com/8cy3D7m
How much difference in intensity is needed to be correct with Cell-to-Cell-Variations? Or was the professional wrong?

I would be hesitant to call that variation as all strongly stained cells are in the bottom left part of the image. That makes me think it's possible (likely) that the plate was not perfectly adjusted when imaging, and that the cells were imaged at different focal planes, e.g. the stronger green ones were imaged more in the middle of the nucleus, making the staining appear stronger, and the weaker ones at higher up/lower > making the staining appear less strong.

Thanks for the explanation.

But for me it raises a problem: How can I decide if the visible varaitions in the staining are a result of the technical imaging-process or the staining itself?

I had an image analysed by a professional today:http://imgur.com/8cy3D7m
How much difference in intensity is needed to be correct with Cell-to-Cell-Variations? Or was the professional wrong?

I would be hesitant to call that variation as all strongly stained cells are in the bottom left part of the image. That makes me think it's possible (likely) that the plate was not perfectly adjusted when imaging, and that the cells were imaged at different focal planes, e.g. the stronger green ones were imaged more in the middle of the nucleus, making the staining appear stronger, and the weaker ones at higher up/lower > making the staining appear less strong.

Thanks for the explanation.

But for me it raises a problem: How can I decide if the visible varaitions in the staining are a result of the technical imaging-process or the staining itself?

If you see a certain variation pattern only in part of the image, I wouldn't trust it. But, for the image you posted, if there had been a strong nucleus in eg upper right corner, it would be much more trustworthy. You can also turn on the red to see whether it looks similar for all cells - are the cells looking ok, or do some have granular red pattern, or look weird in some way? (>> don't trust them). By using the red channel you can also more easily tell whether the focal plane for the different cells seems to be similar.

For other variation patterns, eg if you have nucleus + nucleoli in lower left part of the image, but only nucleus for the rest, I would classify it as variations (as long as it's more than 1 cell - "1 cell is no cell") as it could be that very few cells show that variation, or that the difference in focal plane makes the nucleoli not visible in part ot the image.

I don't mind my accuracy going down (or not going up) if I screw it up, but not when I'm right.Can someone explain to me why cytokinetic bridge is not a correct answer here?

There is a great cytokinetic bridge there!! However it isn't glowing green and that's what you're looking for. They use dye that bonds to different parts of the cell, so don't pick something if it isn't bright green.

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